New Publicly Available Chemical Query Language, CSRML, To Support Chemotype Representations for Application to Data Mining and Modeling

Chemotypes
are a new approach for representing molecules, chemical
substructures and patterns, reaction rules, and reactions. Chemotypes
are capable of integrating types of information beyond what is possible
using current representation methods (e.g., SMARTS patterns) or reaction
transformations (e.g., SMIRKS, reaction SMILES). Chemotypes are expressed
in the XML-based Chemical Subgraphs and Reactions Markup Language
(CSRML), and can be encoded not only with connectivity and topology
but also with properties of atoms, bonds, electronic systems, or molecules.
CSRML has been developed in parallel with a public set of chemotypes,
i.e., the ToxPrint chemotypes, which are designed to provide excellent
coverage of environmental, regulatory, and commercial-use chemical
space, as well as to represent chemical patterns and properties especially
relevant to various toxicity concerns. A software application, ChemoTyper
has also been developed and made publicly available in order to enable
chemotype searching and fingerprinting against a target structure
set. The public ChemoTyper houses the ToxPrint chemotype CSRML dictionary,
as well as reference implementation so that the query specifications
may be adopted by other chemical structure knowledge systems. The
full specifications of the XML-based CSRML standard used to express
chemotypes are publicly available to facilitate and encourage the
exchange of structural knowledge.